The prediction of antigenic determinants is a difficult and uncertain task. Antibody:antigen interfaces have been generally assumed to be hydrophilic and transiently accessible to the surrounding milieu bathing the antigen and, as such, distinct from the subunit:subunit interface of multimeric protein complexes. These assumptions were the basis for the original Hopp and Woods predictive algorithm that sought to identify hydrophilic stretches in the protein linear sequence (Hopp, 1993). This was accomplished by assigning a hydrophilicity value for each of the 20 amino acids and calculating an average score for hexapeptides along the sequence of the antigen. Since then, numerous improved predictive algorithms have been published (Hopp, 1993; Hofmann et al, 1987; Pauletti et al, 1985; Van Regenmortel et al, 1994). Measuring the partition of model synthetic peptides in HPLC analyses has developed empirical hydrophilic values (Parker et al, 1986). Parameters for flexibility (Hopp, 1984), accessibility (Jones et al, 1997) and even antigenicity (Welling et al, 1985) have been introduced in an effort to increase the success rate for accurate prediction of binding surfaces (Van Regenmortel, 1999). Van Regenmortel, who has contributed much to this field, has published numerous detailed and comprehensive reviews and comparisons of predictive algorithms (see, for example, Van Regenmortel, 1999).
The essence of these studies goes towards attempting to learn the fundamental rules for biorecognition and to apply this knowledge to discover potential epitopes of a given antigen. The initial approach has dealt with the linear aspect of protein antigens and is unable to address the more realistic situation of conformational epitopes. Ninety percent of all epitopes are predicted to be discontinuous and highly conformational (Van Regenmortel, 1996). Van Regenmortel has argued that even a three dimensional analysis is still insufficient as one must also consider the fourth dimension—time, which plays a role in the conformational induced-fit of the epitope to better conform to its corresponding paratope of the antibody, and vice versa (Van Regenmortel, 1996).
A major step forward in understanding the nature of the epitope has been due to the co-crystallization of antibody:antigen complexes and solution of their structures at high resolution. Thus, as opposed to the original notion that antigen binding surfaces should comprise only 5-7 amino acid residues (Kabat, 1968), B cell-epitopes are now considered to contain 15-20 residues derived from 2-5 peptide segments of the antigen, occupying a surface of 700-900 Å2 (Lo Conte, 1999; Chakrabarti et al, 2002; Jones et al, 1997). Furthermore, epitopes have been found to incorporate hydrophobic and aromatic residues in addition to hydrophilic and charged amino acids (Glaser et al, 2001). The degree of conformational comp33333lementarity between the epitope and paratope is less complete than might have been expected and water molecules play a significant role in bridging the binding surfaces and “filling-in the gaps” (Xu et al, 1997).
An effective humoral response towards an infectious agent is the ability of antibodies to bind and inactivate the pathogen. Vaccines, designed to induce the production of such antibodies, are typically derivatives of the pathogen, i.e., killed whole cells, attenuated live pathogens, fragments of antigens or DNA corresponding to the latter (Ellis et al, 2001; Hansson et al, 2000). Whatever the modality, the purpose of the vaccine is to stimulate neutralizing immunity in the naive individual in preparation of future encounters with fully virulent field-isolates of the pathogen. Correspondence between the vaccine and the field-isolate of the pathogen must be substantial, therefore, to ensure its efficacy. In cases where the pathogen undergoes extensive genetic variation, the ability to formulate an effective vaccine may present what appears to be an insurmountable obstacle. Such seems to be the case, for example, for HIV-1, the etiological agent of the AIDS epidemic, that is continuously selected for its ability to evade immune surveillance (Burton et al, 1998; Montefiori et al, 1999; Hoffman-Lehman et al, 2002).
HIV-1, as a result of each infectious cycle, accumulates numerous random mutations providing it with an endless source of variants (Wang et al, 2002; Moore et al, 2001). Nonetheless, over the years a few examples of highly cross-reactive and neutralizing monoclonal anti-HIV antibodies have been described—illustrating that protective immunity is possible (Mascola et al, 1999; Gauduin et al, 1997; Burton et al, 1994; Zwick et al, 2001b; Muster et al, 1993; Trkola et al, 1996; Conley et al, 1994; Van Regenmortel, 1996). This has been substantiated by experiments in which cocktails of mixtures of these mAbs, administered as passive immunotherapy, have proven effective in preventing the infection of CD4+ lymphocytes both in vitro and in vivo (Mascola et al, 1999; Gauduin, 1997).
Thus, a rational approach to the design of a cross-reactive antibody response against AIDS can be proposed as follows:                First, one must accumulate a collection of genuine broadly cross-reactive and neutralizing mAbs (to date at least 4 exist (Burton et al, 1994; Zwick et al, 2001b; Muster et al, 1993; Trkola et al, 1996; Conley et al, 1994)).        These, in turn, are used to discover their corresponding epitopes within the antigens of HIV-1.        Once mapped, the epitopes are to be reconstituted as synthetic versions that must be both antigenic (i.e., recognized by the original mAbs) and immunogenic (i.e., able to elicit in the naive individual the production of antibodies that are as effective as the original mAbs themselves).        
Unfortunately, such a protocol turns out to be a very difficult task as the “interesting” mAbs against HIV-1 (and in fact against most pathogens) typically correspond to highly conformational epitopes that are comprised of discontinuous segments of the viral antigen (Van Regenmortel et al, 1996). Very often, even linear epitopes show conformational preferences and dependence on the context of a protein antigen (Ho et al, 2002). Thus, one is faced with a fundamental problem, namely: how can one discover the precise molecular design of conformational discontinuous epitopes of highly desirable mAbs of clinical importance?